The Third
by youngdestiny
Summary: AU. Percy's kidnapped as a young boy, and experimented on by Valentine. When his adoptive brother, Johnathon, is taken over by his demon blood, he escapes from his prison to seek the help of the 'Angel-boy' at the New York Institute. But should he reveal his true identiy? Will they trust him enough to help him?
1. Prologue

_Prologue_

Valentine Morgenstern was standing in a park next to a river, thinking about the wife that had left him, when a boy of four years or so caught his attention.

The boy had his back to him and all he could see was the pitch black hair on his head and the frail body with small hands reaching out to play with the water of the river. The mother was nowhere in sight, so he started to slowly walk closer to the boy, trying to see what he was doing and to see the child's face.

As he got closer he saw what looked like little animals made of water running around the boy and up his arms and legs.

The little boy giggled and laughed in delight, sparkling emerald green eyes lighting up as he smiled in happiness. More miniature animals jumped from the river of water into his lap. An animal, a rabbit, jumped up to his shoulder and looked as if it was whispering in his ear.

Suddenly, his head lifted and he looked in Valentine's direction. Valentine walked forward and he stopped in front of the boy. He, the boy, smiled up at him shyly and lifted a small turtle made of water up and asked, "Pway wif me?" with big eyes.

Valentine crouched down and took the proffered turtle into his hands. However, when the turtle left the boy's hands, it dissolved into water and dripped between Valentine's fingers, falling softly to the ground. He looked on as the boy pouted at the water and to the boy's delight another turtle slowly climbed out of the river and onto the boy's waiting hand.

Valentine looked at the boy curiously and asked, "What's your name, little one?"

The boy looked up at him. "Pewcy!" he answered and went back to playing with his water animals.

"My name is Valentine," he said and a predatory grin slowly stretched across his face. "You know, I have a son your age, whom I'd like you to meet…."

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**Author's note: **

**Hey guys! This is my first fic. I like to read fanfiction so I wanted to try and write my own. Hope you enjoyed the first part and I will continue this story, even though updates will be slow. Thank you to my beta, Tala White 14, for helping me. **


	2. Chapter 1

_9 years later_

Cold, damp air and the sound of chains clanking together surround him. Percy Morgenstern was chained to the wall, shackles around his ankles and wrists. He was 13 now and still wasn't let out of the basement. His brother, Jonathan, would sometimes sneak in to keep him company or try to clean his wounds. Even though his brother had demon blood running through his veins, he still had some humanity left.

Suddenly, the door to the basement creaked open and dim light streamed in as exhausted emerald green eyes lifted to look at the man he had thought of as a father.

He was only six when his father brought him down to the basement to show him his experiments. When he was done bragging and explaining to a horrified Percy, looking proudly at his experiments, he grabbed Percy from behind and shoved him into a cage.

He was eight when his father deemed him old enough and injected him with werewolf DNA. As he lay there, in pain, his father explained to him that 'why shouldn't Shadowhunters have the powers of Downworlders' and 'he was going to make Percy special and more powerful'.

Five years and a vampire DNA injection later, he's here, right where his father had left him. His brother stopped visiting him when Percy turned twelve, _'Jonathan probably lost it or Valentine had caught him' _he had thought_. _

Valentine slowly descended from the stairs and walked to him at a sedated pace, looking him up and down. "Well my son, looks like it's time. You're going to learn, I'm going to teach and you are going to give it your all. Do you understand?" He stopped in front of Percy and looked him in the eyes.

Seeing Percy's faint nod, he slowly started to unshackle him. When Valentine was done, Percy dropped to the ground and landed into a groaning heap on the floor. He tried to get up, but his knees kept giving in until strong hands wrapped around his arms and hauled him to his feet.

"Come." He said and dragged Percy up the stairs of the basement, still keeping a firm hand around his arm.

As Percy stepped out of the basement, he covered his eyes with an arm to block the sharpening light and took another step into his childhood house.

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**Author's Note:**

**Hey guys, next chapter will be a two year time skip where Percy will be 15 and fully trained. **


	3. Chapter 2

_Two years of training later_

Jonathan and Percy sat together on one of the couches and Valentine sat in an armchair opposite of them. Jonathan had a cold smirk on his face and Percy just had a blank look on his face. Valentine sat there with a calculating expression, studying them carefully. _Who should I trust more? Which one can I control best? Hmm…._

"Jonathan, I would like to take you with me. Go get the necessary things and pack them," Valentine ordered him with a deep voice. With an irritated sigh and anger flashing in his eyes, Jonathan stood up and walked out of the room. "Percy, you will stay here and you will not step a foot out of this house, understand?" he looked Percy up and down with scowl on his face.

Two years of training and Percy had gained a lot of muscle. His hair had grown to his shoulders and was currently tied together at the nape of his neck with a piece of leather. He had grown a lot stronger and could take on almost anyone. Although every time he and Jonathan fought, they ended up with a draw.

His once brilliant emerald eyes were dull and stared stoically right back at Valentine, daring him to insult Percy. Valentine cleared his throat and stood up, also leaving the room. As he exited, Percy heard him mutter under his breath, "Rather safe than sorry."

_15 minutes later (In the basement) _

He was once again chained to the wall but this time Valentine was drawing runes on the floor with Jonathan standing at the door, arms crossed and waiting. Next to him, in the corner of the room, was the angel Ithuriel, chained up and lying in a circle of runes and an invisible barrier keeping him inside and from using any of his powers.

"This will keep you from escaping. Don't try doing anything stupid to get out; you'll only hurt yourself and I might need to use you in the future. So try not to do too much damage to yourself." Valentine said, standing up and walking to the door where Jonathan pushed off from the wall. Jonathan gave Percy one last sneer and said, "Goodbye, _little brother_."

He turned around and followed Valentine out the door of the basement, the door closing with a squeak and a grunt. The sound of locks sliding and clicking into place reached his ears and he hung his head in defeat.

He didn't know what went wrong with his brother. They used to be so close. Jonathan used to be caring and like a big brother to Percy. Sure, he became a little weird and violent when they played games, but he never looked at Percy with hatred in his eyes.

He was eleven when Jonathan only came once a week to visit him in the basement. Then it became once a month and then he rarely saw his brother at all. Jonathan became even more violent and maybe even a little crazy. When Percy was twelve, Jonathan came bursting into the basement with a wild look in his eyes and started hitting him.

He heard his dad and Jonathan sometimes talking about a boy named Jace. Valentine kept telling Jonathan that he was better than Jace, stronger than Jace and more skilled than Jace, but Percy couldn't help but feel that it wasn't the whole truth. They talked about how he was too nice and cared too much about others. Percy remembered how Jonathan would fly into an intense rage, whenever he asked him about this other boy. "The little Angel-Boy? He's a pathetic weakling." Percy didn't know what went wrong; he only wanted his brother back.

A fragment of an idea sparked in his mind. His head whipped up as his heart filled with hope. He might not know who Jace was, but if the boy was as good as Valentine said he was, maybe he could help Percy get his brother back. In his eyes determination flashed.

Even if he couldn't find and convince Jace to help him, he would escape. He would save his brother, no matter what.

* * *

**Author's Note:**

**Hey! I want to thank those who had reviewed and thank you for all the compliments. I'm going to try and write in Percy's point of view the next chapter, but I'm not making any promises. This story from the third chapter on is going take place in City of Glass. The prologue was in the time of City of Bones, and the second chapter in City of Ashes. My updates will be a bit slow because I'm starting with exams and need to start studying. Again, thank you to my beta, Tala White 14. **


	4. Chapter 3

**Chapter 3**

'I have to get out of here' he thought, pulling at the chains and staring at the runes on the floor around him. He hasn't fed for days but could at least break the chains; he wasn't sure about the runes. **_{Break the floor.} _**a voice sounded in his head and he looked at the angel in the corner of the basement. **_{Think about the earth beneath your feet and imagine a crack appearing and breaking the rune circle.} _**Ithuriel explained and looked away at the end of his sentence.

Percy pulled and tugged at the chains on his ankles and around his wrists. The chains broke with a screeching sound and fell to the floor. As he finished rubbing his wrists, he closed his eyes and imagined the circle of runes with a crack running through it. Suddenly, the ground started shaking and he heard a loud ripping sound with a crack. He opened his eyes and looked at the ground, seeing that it had worked.

Jogging halfway to the door before stopping, he looked at the Ithuriel. **_{Leave, do not worry about me.} _**the angel said, answering the silent question in Percy's eyes. Running to the door he started pulling and tugging on the handle. **_{Go save your brother.} _**and with a screech and a bang the door flew open and darkness greeted him.

He has been running for what felt like ours, when he finally stopped at the blue shimmering border of Idris. 'How am I going to get out of here?' he thought, going through everything he knew about the border and searching for any flaws. 'I have to get out of here! ' he thought and suddenly his body turned into mist.

He landed on his hands and knees on cold, hard pavement. Slowly he stood and brushed off his hands and knees. Lifting his head he saw the most breathtakingly beautiful building ever. The walls were pure white, pillars with angels and patterns carved into them and a huge wooden door with the angelic rune carved into it. He stood there, staring at every detail in awe and slowly started to walk towards the door.

He stopped in front of it and traced the rune with the tips of his fingers. 'Now how do I get in?' he thought and took a step back, staring at the door with a frown. Suddenly, he had a feeling to do something, something urging him to do it. He lifted his hand to his mouth, letting his fangs descend and tore a line across his palm. Blood dripping down his fingers, he lifted his hand and placed his palm against the door. As the moonlight shone down upon him, his blood glittered with a golden sheen.

The doors slid open smoothly and stopped with a soft thud. He walked into the building with caution in his steps and the doors closed behind him. Moving down the short corridor towards the elevator, he stopped when he heard a soft scraping sound.

He turned his head slightly to the left to see what had made the sound. Suddenly, out of nowhere a grey thing hurled itself at Percy and clung to his face. Claws dug into his cheekbones and scalp as he tried to pull the creature off of him. Finally he got the little demon off and threw it as far away from him as he possibly could.

Unfortunately the little bugger came running back, faster than anything he has ever seen before and jumped; now clinging to his leg. "Get off you crazy fur ball!" he yelled and shook his leg, _trying _to get it off but failing miserably. Grabbing the thing underneath its arms he pulled and pulled. 'Damn, this demon's stretchy!' he thought as he tugged on it a little more.

Suddenly, it let go and jumped at his face, swiping at him with its claws. Grabbing and holding it at arm's length, he studied the demon closely. Only to realise- "_What _are you doing to my _cat_?" a girl's voice suddenly asked.

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**Author's Note: **

**Thank you to all of you who reviewed, I ****_really_**** appreciate it! I'll really try to make the chapters longer and it probably will later on. I'm not sure if I'm going to bring some demigod characters in. As I said in the first chapter, the updates will be a bit slow because I'm going to start with exams soon. If a sentence or word sounds weird or there's a spelling mistake, sorry, I didn't have my beta this time! Thank you all who read this and please leave a review! ;) **


	5. Chapter 4

**Chapter 4**

"What are you doing to my cat?!" a girl asked, walking down the few steps in front of an elevator, towards me. I studied the demon closely, only to realise that she was right, it was a cat!  
Dropping the cat, it gave a frantic yowl when it landed awkwardly on its butt. Clearly not all cats land on their feet. That is… if it really was a cat.

I kept my gaze narrowed suspiciously until the scampering creature disappeared from view. Then I shuddered and rubbed my hands furiously on my hoody. Demon pox was always a possibility.

Looking back at the girl I saw that she was staring at me with an eyebrow raised in question of my sanity. "Don't want cooties." I offered as explanation, making the eyebrow arc even higher.

"Who are you and what are you doing here?" she asked suspiciously.

"I…um…I'm Percy." I said slowly, uncertain about telling her my true name.

"Do you want a room to stay for, like, a few weeks or longer?" she asked with a hint of exasperation and total boredom in her tone.

"Longer. I'm hunting something specific." I reply thinking of how long it will take me to get them to trust me enough to help me save my brother. It wouldn't seem too suspicious if she knew I had a reason to be here. Most Shadowhunters would simply be passing through, yet it wasn't unheard of for one to stay longer if they had a vendetta. And in the demon hunting business, vendettas were as common as hearts in February….

_Sheesh, worst comparison ever!_ I scolded myself mentally.

She nodded, straightened her shoulders and spun around on her high heeled boots. With her back to me, she walked towards the elevator and demandingly barked, "Come!" I ran after her, not wanting to disobey her order, in fear of what she might do to me with that lovely whip curled around her arm.

She stepped inside the elevator with me right beside her. Closing the elevator doors, it squeaked and screeched. Worse than a certain demon (or cat… yeah, probably not) I just had the pleasure –and pain- of meeting. The elevator started moving with such a massively hard, jerk that I almost face-planted into the mirror in front of me. Not that I mind seeing my face up-close.

Finally, after a rather bumpy ride, the elevator stopped with a loud bang and another big jerk. The doors screech open as if in pain, and we stepped outside into the cold, dark passageway. "Alright, follow me." She said. We walked down a few corridors and stopped at passageway with doors left and right. "Well, here we are. Just pick any room you'd like, except those three. By the way, the name's Isabelle." She said and pointed at three doors and then at herself. I walked to a random door and walked inside, looking around. Not bad, a closet, bed, nightstand, chest of drawers, mirror and a bathroom. It's a lot better than my previous 'room' *cough* basement *cough*.

"Do you want me to introduce you to everyone?" Isabelle asked. I nodded and she motioned for me to follow. We finally ended up at the library. Birds in flight were carved into the wood of the doors, vines growing from bottom to the top. It looked like they were reaching for the birds, wanting their freedom of flight. She opened the doors and peeked inside. "Huh, looks like they're not here. Maybe in the weapons room?" she came back out and shut the doors behind her, shaking her head and she seemed to be muttering to herself. I raised an eyebrow, looking at her, but she didn't even glance my way. She was talking to herself like she forgot I was here. And she questioned _my _sanity?

We walked down the corridor and around a bend, stopping in front of another door. This one had two swords carved into the wood with very fine attention to detail and had ribbons tied to their hilts. She opened the doors and walked in with me following her. There were two boys standing over a table and seemed to be looking at some kind of weapon.

"Hey guys! Whatcha doin'?" she asked and skipped over to them and peeked over one boy's shoulder. Both boys were wearing black, but one boy had golden blond hair and the other black.

"Figuring out how this thing works." The black haired boy said.

"Actually, he's still trying to figure it out. I've already mastered it, of course." The blondie said, studying his nails.

"Then why don't you just explain it to him?" Isabelle asked, looking as if she already knew the answer.

"I tried!" Blondie said, throwing his hands up into the air. "Five times to be exact! He just won't understand!" he sounded angry, as if he's scolding the other boy.

The black haired one scowled at Blondie. "Well I'm _so _sorry that I can't understand a word you're saying! Forgive me for not being smart enough for you, my lord!" he said, his words dripping with sarcasm.

"Good. You should be." Blondie nodded, sounding very genuine.

Isabelle sighed, putting her hands on her hips and shaking her head. "Well, we have a guest. His name is Percy and he's gonna be around for a while." She said and pointed to me.

The boys turned around and I finally got to see their faces. One had black hair and blue eyes. The other had golden hair and golden eyes.

"Percy, this one's name is Alec –my brother- and Jace –my other brother." She pointed at them as she said their names.

My eyes locked with the boy named Jace. '_Angel-Boy._'

**Author's Note:**

**I am sooooooo sorry! I really wanted to update, I just didn't have time to do it. We emigrated to New Zealand and it is hell on earth people! It's crazy between unpacking, packing and Halloween too! I will really try to update again. But it's exams this week and we're still unpacking and I'm adjusting to the new school. I really hope you'll forgive me! ** **I apologise profusely and I hope you guys/girls still love my story. Enough to at least leave a teeny tiny review. ) **


	6. Chapter 5

Chapter 5

'Wow…it was easier finding him than I thought.' I studied the boy in front of me. Well, he didn't really look like an angel, not like a goody two shoes at all, just bad boy-ish. 'Okay, time to get the show on the road…' I mentally sighed. 'This is gonna take a while.'

"Hey. M' name's Percy." I said with an awkward wave of the hand (more like a spasm.) And they just kept staring at me. _I'm not that interesting. Am I?_

Suddenly Jace took a few steps toward me and leaned in closely. I don't think he knows anything about _personal space._ He studied my face while I tried to lean backwards, so I wouldn't have to cross my eyes to see him. Yeah, he's that close. He nodded his head, seemingly satisfied. "Just a hint, do _not _eat Izzy's food." He said, very seriously.

"Yeah, you might just die. From, like, food poisoning." Alec said as he walked past me and Jace.

"Hey! I heard that!" Isabelle yelled with an indignant look on her face.

After meeting the other interesting occupants of the New York Institute, I wandered the corridors and explored every room. I also went to the library to see what kind of books they have, nothing for kids under 13, that's all I can say. I also discovered a greenhouse above the library on the roof. It's beautiful with all kinds of flowers and plants and it all looked so… green - vibrant.

I turned around, about to leave the library, when Isabelle walked in. "Hey Percy! Wanna go partying with us?" she asked, looking really excited.

"Uh… p-partying? Um, I'm not so sure…" I stammered, fighting the feeling that's telling me to run away.

"Oh, come on! It'll be fun!" she said.

_Fun_? I think not. But it could be interesting and I can even get closer to them then. "Okay." I said and followed her out of the library and to the elevator. We climbed in along with Jace and Alec and I was surprised to see a girl with orange hair, green eyes, lots of freckles and a boy with brown hair and eyes with glasses.

I looked questionably at the three Shadowhunters. "Oh! Percy, this is Clary and Simon. Clary, Simon, this is Percy. We met them a few days back at a club. Percy is a Shadowhunter too, Clary." Isabelle said as she introduced us.

One bumpy ride later, we were outside and walking down the street. "So, where exactly are we going?" I asked while following the two boys in front of the group with Isabelle next to me and Clary next to her with Simon a little bit behind Clary.

"Magnus Bane's house. He's the high warlock of Brooklyn." Isabelle answered, her eyes wide as if revealing something of great import. _Say WHAT_?! High Warlock of Brooklyn?!... Huh, never heard of him.

After a bit of a walk, the two boys in front of us spotted something. We walked quickly to catch up to them. When we got close enough to see what they were looking at, I was surprised. Vampires' bikes.  
"Heh, never thought I would see these in this part of town." Jace said while studying one bike's paint job.

"Okay, wonderful, we're looking at bikes! Can we go now?" Isabelle asked impatiently.

"Go on ahead." Jace said with a mischievous look in his eyes that just _spelled_ trouble.

They caught up with us when we neared the house and we walked up the few steps that led to the door. Jace rang the doorbell and we waited silently. The door was opened rather abruptly by a man with way to much glitter, slitted pupils and strangely enough, he had no pants on.

"Well, I don't remember inviting any Shadowhunters to my party." He said while we continued staring at the pant-less man. "You do know that it's rude to stare." He said and we quickly closed our mouths.

Isabelle wordlessly held out the invitation and the man took it from her. He stared at the piece of paper with a blank look on his face. He casted his eyes heavenward in exasperation and racked a hand through his hair. "I must've been _really _drunk when I handed these invitations out." He said and sighed. "Oh alright, you might as well come in. Please try not to murder any of my guests." He said and stood to the side, opening the door wide.

"Even if they annoy me?" Jace asked with arrogance in his voice.

"Do not test me Shadowhunter." The sparkly man said and his eyes flashed yellow. Oooh..I wanna do that. It looks so cool and, well, flashy.

We entered the house and stared at the crowd. Bodies dancing, some sitting at the bar, some just socialising and of course, a band. Isabelle dragged Simon over to the dance floor as I stood by the door, leaning against the wall next to it. The others talked to the sparkly man, who had introduced himself as Magnus Bane.

I interrupted their conversation by asking Magnus why he was throwing a party. "Well, it's for my cat's birthday, but he mysteriously disappeared." He answered. He took Clary, Jace and Alec upstairs to talk and I watched as Simon and Isabelle danced, doing a good impression of a hyper-active bunny and a convulsing snake.

A while later Isabelle dragged Simon over to the bar. The others haven't come down yet, so I waited some more. Suddenly I heard Isabelle yell Simon's name. I ran over to her where she was kneeling, looking under the bar.

"What's wrong?" I asked.

"He drank the blue drink when I told him not to drink the blue drink and he turned into a rat!" Isabelle exclaimed.

Ooh, Clary's not gonna be happy. In the end, Isabelle ran to get the others, told them about what happened, Clary yelled at Isabelle and Clary got Simon out from underneath the bar. Isabelle went to find Magnus, Clary asked Magnus to turn Simon back, turns out he can't but "_I swear it will wear off_." He flirted with Alec and we left.

Halfway back to the institute, Clary and Jace suddenly stopped walking and fell behind. I stopped the others who were walking in front of me and looked back at the other two. "Hey! You two okay back there?" Alec shouted.

Jace looked up as Clary continued to search for something in her backpack. "We're fine! Go on ahead!" Jace answered.

"Oh hell no." Isabelle grumbled and started walking back to Clary and Jace.

"He's gone! Gone!" Clary yelled and almost dropped her backpack in her panic.

"Who're you talking about?" Alec asked.

"Simon!" Clary screamed in his face. _I don't like her_, I thought. Jace grabbed her by the shoulders, shook her a bit and they started talking in hushed tones.

Finally, Jace looked up at us. "Okay, we're gonna go find Rat Boy." Jace declared. Clary gave him a looked and hissed out the name 'Simon' to him.

"Okay." Isabelle said casually and shrugged with her hands on her hips.

"Where are we going?" Alec asked.

"The Hell Hotel of Vampires…"

**Author's note: **

**Sorry I took so long to update, I just didn't know what to write for this chapter. Anyway, I decided not to bring any other demigods into this story, just Percy. I hope you all have a wonderful year and good luck with school 2015! **


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